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- PDB-2xdb: A processed non-coding RNA regulates a bacterial antiviral system -

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Basic information

Entry
Database: PDB / ID: 2xdb
TitleA processed non-coding RNA regulates a bacterial antiviral system
Components
  • TOXI
  • TOXN
KeywordsTOXIN/RNA / TOXIN-RNA COMPLEX / ABORTIVE INFECTION / PHAGE
Function / homology
Function and homology information


plasmid maintenance / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / negative regulation of DNA-templated transcription / RNA binding / identical protein binding
Similarity search - Function
ToxN/AbiQ toxin / Toxin ToxN, type III toxin-antitoxin system / Thiol Ester Dehydrase; Chain A - #130 / Thiol Ester Dehydrase; Chain A / Roll / Alpha Beta
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / Endoribonuclease ToxN
Similarity search - Component
Biological speciesPECTOBACTERIUM ATROSEPTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBlower, T.R. / Pei, X.Y. / Short, F.L. / Fineran, P.C. / Humphreys, D.P. / Luisi, B.F. / Salmond, G.P.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: A Processed Noncoding RNA Regulates an Altruistic Bacterial Antiviral System.
Authors: Blower, T.R. / Pei, X.Y. / Short, F.L. / Fineran, P.C. / Humphreys, D.P. / Luisi, B.F. / Salmond, G.P.C.
History
DepositionApr 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TOXN
G: TOXI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,28712
Polymers32,5492
Non-polymers73810
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-120.8 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.650, 183.650, 183.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

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Components

#1: Protein TOXN


Mass: 19726.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PECTOBACTERIUM ATROSEPTICUM (bacteria) / Strain: SCRI 1039 / Description: ENVIRONMENTAL ISOLATED FROM SCOTLAND, U.K / Plasmid: PTYB1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: B8X8Z0, EC: 3.1.27.3
#2: RNA chain TOXI /


Mass: 12822.509 Da / Num. of mol.: 1 / Fragment: BACTERIA ANTITOX, RESIDUES 1775-1814
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PECTOBACTERIUM ATROSEPTICUM (bacteria) / Strain: ECA SCRI 1039 / Description: ENVIRONMENTAL ISOLATED FROM SCOTLAND, U.K / Cell line: ER2566 / Plasmid: PACYC184 / Production host: ESCHERICHIA COLI (E. coli) / References: GenBank: FJ176937
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsA23: RNA IS CLEAVED BY TOXN (CHAIN A IN THE STRUCTURE) AT A-32, AND FORMING 2'3'-CYCLOPHOSPHATE-A.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 0.55 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.01M COCL2, 0.1M MES PH6.5, 1.8M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9702
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 8, 2009 / Details: SINGLE SILICON (111) MONOCHROMATOR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9702 Å / Relative weight: 1
ReflectionResolution: 2.55→75 Å / Num. obs: 18604 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 20 % / Biso Wilson estimate: 62.05 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.9
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XDD

2xdd


Resolution: 2.55→45.91 Å / SU ML: 0.47 / σ(F): 1.52 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 1630 5 %
Rwork0.176 --
obs0.178 32638 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.43 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 73.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 764 26 100 2206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092214
X-RAY DIFFRACTIONf_angle_d2.5633161
X-RAY DIFFRACTIONf_dihedral_angle_d20.486964
X-RAY DIFFRACTIONf_chiral_restr0.08376
X-RAY DIFFRACTIONf_plane_restr0.009267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5502-2.62520.38711370.32632612X-RAY DIFFRACTION100
2.6252-2.710.32241380.29212553X-RAY DIFFRACTION100
2.71-2.80680.33261240.26392582X-RAY DIFFRACTION100
2.8068-2.91920.32341250.24972615X-RAY DIFFRACTION100
2.9192-3.0520.27471500.21132568X-RAY DIFFRACTION100
3.052-3.21290.20561050.17652597X-RAY DIFFRACTION100
3.2129-3.41410.21161170.16342624X-RAY DIFFRACTION100
3.4141-3.67760.1891430.14952566X-RAY DIFFRACTION100
3.6776-4.04750.15721060.12672596X-RAY DIFFRACTION100
4.0475-4.63270.15521590.10862575X-RAY DIFFRACTION100
4.6327-5.83490.14121590.12172549X-RAY DIFFRACTION100
5.8349-45.920.21011670.17512561X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5144-0.1561-0.60910.37740.26122.1788-0.2048-0.0118-0.0948-0.05150.03050.16640.1931-0.11520.11740.305-0.1004-0.01250.26660.1170.32946.8017-13.004631.0309
20.8937-0.289-0.26671.4894-0.97250.96180.0654-0.09-0.3553-0.05330.08920.1920.1088-0.2183-0.1740.40120.0258-0.26470.39080.08020.5392-10.89936.600118.5708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN G

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